build.js

var webpack = require('webpack');
var config = require('./webpack.config');

var configs = [
  config({
    entry: {
      head: ['app/assets/js/head.js')],
    },
    outputFile: '[name].js',
    chunkFile: '[name].js',
  }),

  config({
    entry: {
      tail: [
        'babel-polyfill',
        'app/assets/js/tail.js'
      ]
    },
    outputFile: '[name].[hash].js',
    chunkFile: '[name].[chunkhash].js',
  })
];

configs.forEach(function(conf) {
  webpack(conf, function(err, stats) {
    // ...
  });
});

webpack.config.js

module.exports = function(config) {
  var loaders = [
    {
      loader: 'babel',
      test: /\.jsx?$/,
      include: [
        /app\/assets\/js/,
        /fmjs/,
      ],
    },
    // ...
  ];
  
  var webpackConfig = {
    middlewarePublicPath: '/assets/js/',
    entry: config.entry,
    output: {
      filename: config.outputFile,
      chunkFilename: config.chunkFile,
      path: 'public/assets/js',
    },
    module: {
      loaders: loaders,
    },
    devServer: {
      host: 'localhost',
      port: 8080,
    },

    // ...
  };

  return webpackConfig;
};